Genomics of pear and other Rosaceae fruit trees

The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry.     

Fine mapping of the gene for susceptibility to black spot disease in Japanese pear (Pyrus pyrifolia Nakai)

Black spot disease, which is caused by the Japanese pear pathotype of the filamentous fungus Alternaria alternata (Fries) Keissler, is one of the most harmful diseases in Japanese pear cultivation. We mapped a gene for susceptibility to black spot disease in the Japanese pear (Pyrus pyrifolia Nakai) cultivar ‘Kinchaku’ (Aki gene) at the top of linkage group 11, similar to the positions of the susceptibility genes Ani in ‘Osa Nijisseiki’ and Ana in ‘Nansui’. Using synteny-based marker enrichment, we developed novel apple SSR markers in the target region. We constructed a fine map of linkage group 11 of ‘Kinchaku’ and localized the Aki locus within a 1.5-cM genome region between SSR markers Mdo.chr11.28 and Mdo.chr11.34. Marker Mdo.chr11.30 co-segregated with Aki in all 621 F₁ plantlets of a ‘Housui’ × ‘Kinchaku’ cross. The physical size of the Aki region, which includes three markers (Mdo.chr11.28, Mdo.chr11.30, and Mdo.chr11.34), was estimated to be 250 Kb in the ‘Golden Delicious’ apple genome and 107 Kb in the ‘Dangshansuli’ Chinese pear genome. Our results will help to identify the candidate gene for susceptibility to black spot disease in Japanese pear.     

Nationwide seroprevalence of Neospora caninum among dairy cattle in Japan

Serum samples from 2420 clinically healthy dairy cattle, randomly selected from stored sera in 18 districts of Japan, were tested for the presence of Neospora caninum antibodies using an indirect fluorescent antibody test (titer > or =1:200). Nationwide seroprevalence is estimated at 5.7% (139/2420). Seropositive cattle were detected in all surveyed districts despite the evidence of confirmed case reports of bovine neosporosis, showing that N. caninum is widely distributed throughout Japan. Age-specific seroprevalence did not increase with cattle age, suggesting that Neospora infection is likely to be transmitted vertically rather than horizontally in Japan. Considering that N. caninum seropositive cows are thought to be more likely to abort, substantial fetal losses may be induced by N. caninum infection in Japan. Devising strategies are needed to reduce the economic impact on the Japanese dairy industry. This is the first study to investigate the nationwide seroprevalence of N. caninum in cattle in Asia.     

Real-time observation and prediction of physical processes in a typhoon-affected lake

A nowcasting system integrating observations and a numerical model was developed to better understand the spatial distributions and temporal variations in the dynamics of a small, subtropical lake occasionally influenced by severe rainstorms. The nowcasting system was used to monitor real-time meteorological conditions and thermal structures, to provide spatial information on the thermal and flow dynamics from model predictions, and to compare the predictions with the observations. The system was also able to determine whether the instruments collecting field data were performing correctly using telemetry operations. The nowcasting system was initially operated in the spring of 2009 in Yuan-Yang Lake, Taiwan. Rainstorm-induced mixing occurred due to Typhoon Morakot during August 7–9, 2009. The mixing was observed by the instruments, and the spatial distributions and temporal variations during the mixing were successfully predicted by the three-dimensional hydrodynamic lake model. A quantitative comparison of the energy balances among the heat, wind, and water inflow inputs to the lake implied that the typhoon-induced mixing was primarily caused by strong winds. The model predictions showed that the lake experienced mixing and flooding (large amounts of inflow/outflow discharges), resulting in homogenous temperatures and flows that moved to the outlet of the lake.     

Vertical behavior of bigeye tuna (Thunnus obesus) in the northwestern Pacific Ocean based on archival tag data

The behavior of bigeye tuna (Thunnus obesus) in the northwestern Pacific Ocean was investigated using archival tag data for 28 fish [49–72 cm fork length (FL) at release, 3–503 days] released in Japanese waters around the Nansei Islands (24–29°N, 122–132°E) and east of central Honshu (Offshore central Honshu, 32–36°N, 142–148°E). Vertical behavior was classified into three types based on past studies: ‘characteristic’ (non‐associative), ‘associative’ (associated with floating objects) and ‘other’ (behavior not fitting into these two categories). The proportion of fish showing associative behavior decreased and that of characteristic behavior increased as fish grew, and this shift was pronounced at 60–70 cm FL. The fish usually stayed above the 20°C isotherm during the daytime and nighttime when showing associative behavior and below the 20°C isotherm during daytime for characteristic behavior. A higher proportion of characteristic behavior was seen between December and April around the Nansei Islands, and between September and December for offshore central Honshu. Seasonal changes in vertical position were also observed in conjunction with changes in water temperature. In this study, ‘other’ behavior was further classified into five types, of which ‘afternoon dive’ behavior, characterized by deep dives between around noon and evening, was the most frequent. The present study indicated that in the northwestern Pacific Ocean, the vertical behavior of bigeye tuna changes with size, as well as between seasons and regions.     

The <Emphasis Type="Italic">Arabidopsis NST3/SND1</Emphasis> promoter is active in secondary woody tissue in poplar

Wood biomass is one of the promising future materials for biofuels with no competing food uses. However, the higher cost to produce bioethanol from wood feedstocks is regarded as a priority issue. Genetic engineering techniques have been proposed to enhance the quality and quantity of wood materials to overcome the cost problem. Although many genetically engineered trees with applicable traits such as low lignin, a high syringyl to guaiacyl ratio and high cellulose content are generated, ectopic expression of an effector gene under a constitutive promoter can sometimes induce untoward side effects on plant growth and development. Our recent study demonstrated that AtNST3/SND1 promoter of Arabidopsis thaliana is a candidate tool for driving a potent activator to enhance wood biomass production in poplar without any growth retardation. However, the tissue- and cell-dependent activity of the promoter remains to be elucidated. In the present study, we generated transgenic poplar expressing AtNST3/SND1promoter::GUS to examine in detail the activity of the AtNST3/SND1 promoter. Histochemical analysis revealed that the promoter was predominantly active in secondary woody tissue. Our result indicates that the AtNST3/SND1 promoter is an option for expressing an effector gene to modify secondary cell wall components and wood biomass.     

Class I hydrophobin BcHpb1 is important for adhesion but not for later infection of <Emphasis Type="Italic">Botrytis cinerea</Emphasis>

Hydrophobins are small secreted proteins unique to filamentous fungi. In this study, we cloned and characterized the class I hydrophobin gene BcHpb1 in the necrotrophic pathogen Botrytis cinerea. The BcHpb1 protein consisted of 117 amino acids. Similar to class I hydrophobins from other fungi, BcHpb1 contains eight conserved cysteine residues. The hydropathy plot of the BcHpb1 amino acid sequence was characteristic of a class I hydrophobin. These results indicated that the BcHpb1 gene encodes a class I hydrophobin. Vegetative growth of ΔBcHpb1 strains, null mutants of BcHpb1, was similar to that of the wild-type strain as were the conidiophores, conidia, appressoria and virulence on host plants. However, adherence of ΔBcHpb1 strains to hydrophobic surfaces was greatly reduced, implying that BcHpb1 is important for the hydrophobicity of conidia and that BcHpb1 may be required to adhere to plant surfaces under certain environmental conditions.     

Mutation analysis of barley malt protein Z4 and protein Z7 on beer foam stability

Beer foam stability is an important characteristic. It has been suggested that isoforms of protein Z, that is, protein Z4 and protein Z7, contribute to beer foam stability. We investigated the relationship between beer foam stability and protein Z4 and protein Z7 using their deficient mutants. As a protein Z4-deficient mutant, cv. Pirkka was used. Protein Z7 deficiency was screened in 1564 barley accessions in the world collection of Okayama University, Japan. The barley samples from normal, protein Z4-deficient, protein Z7-deficient, and double-deficient were genotyped in F(2) populations and then pooled based on the DNA marker genotypes of protein Z4 and protein Z7. For a brewing trial, F(5) pooled subpopulations were used. After malting and brewing, the foam stability was determined, and the results showed that the levels of foam stability in the four samples were comparable. Two-dimensional gel electrophoresis was used to investigate the proteome in these beer samples. The results showed that low molecular weight proteins, including lipid transfer protein (LTP2), in the deficient mutants were higher than those in the normal sample. Our results suggest that the contribution of protein Z4 and protein Z7 to beer foam stability was not greater than that of other beer proteins.     

Effects of polyphenols from seed shells of Japanese horse chestnut (Aesculus turbinata BLUME) on methotrexate-induced intestinal injury in rats

The purpose of this study was to evaluate the effects of polyphenols from seed shells of Japanese horse chestnut (JHP) on methotrexate (MTX)-induced intestinal injury in rats. MTX application caused intestinal morphological injury and increase in malondialdehyde (MDA) levels, decrease in levels of glutathione (GSH) and glutathione peroxidase (GSH-Px) activities in small intestine. However, oral administration of JHP ameliorated MTX-induced intestinal injury and inhibited the increase in MDA and the decrease in GSH and GSH-Px activity in small intestine. In conclusion, our results indicated that oral administration of JHP alleviated MTX-induced intestinal injury through its antioxidant properties.